Talk about a open ended question... 😉
There are a load of apps that will let you view pdfs, from the dedicated pdf reader from Felaur which allows custom bookmarks and file flagging to the more general file viewers like (in no particular order) Air Sharing, Files, Mobile Files, FileMagnet, Datacase (the list goes on) but none will let you edit them or add notes to them.
Likewise, if you wnat to make notes, there are a number of text editors that provide a degree of functions over and above the inbuilt Notes; Evernote, Take a Note, Text Guru (which will read pdf as well).
I suggest you pay the App Store a visit, do a search and read the descriptions and feedback. Should help you narrow it down to what you want.